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import gzip
import os
import pysam
from TestUtils import TABIX_DATADIR
FN_COMPRESSED = "example.bed.gz"
FN_UNCOMPRESSED = "example.bed"
FN_LARGE_COMPRESSED = "example_large.bed.gz"
FN_LARGE_UNCOMPRESSED = "example_large.bed"
def read_python_compressed(fn):
'''iterate through with python.'''
with gzip.open(fn, mode="r") as f:
return len([x.split(b"\t") for x in f])
def read_python_uncompressed(fn):
with open(fn) as f:
return len([x.split("\t") for x in f])
def fetch_plain(fn):
with pysam.Tabixfile(fn) as f:
return len(list(f.fetch()))
def fetch_parsed(fn):
with pysam.Tabixfile(fn) as f:
return len(list(f.fetch(parser=pysam.asBed())))
def iterate_generic_compressed(fn):
with gzip.open(fn) as f:
return len(list(pysam.tabix_generic_iterator(f, parser=pysam.asBed())))
def iterate_generic_uncompressed(fn):
with open(fn) as f:
return len(list(pysam.tabix_generic_iterator(f, parser=pysam.asBed())))
def iterate_parsed_compressed(fn):
with gzip.open(fn) as f:
return len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
def iterate_parsed_uncompressed(fn):
with open(fn) as f:
return len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
def iterate_file_compressed(fn):
with gzip.open(fn) as f:
return len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed())))
def iterate_file_uncompressed(fn):
with open(fn) as f:
return len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed())))
def test_read_python_compressed(benchmark):
result = benchmark(read_python_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
assert result == 164
def test_read_python_uncompressed(benchmark):
result = benchmark(read_python_uncompressed,
os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
assert result == 164
def test_fetch_plain(benchmark):
result = benchmark(fetch_plain, os.path.join(TABIX_DATADIR, FN_COMPRESSED))
assert result == 164
def test_fetch_parsed(benchmark):
result = benchmark(fetch_parsed, os.path.join(
TABIX_DATADIR, FN_COMPRESSED))
assert result == 164
def test_iterate_generic_compressed(benchmark):
result = benchmark(iterate_generic_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
assert result == 164
def test_iterate_generic_uncompressed(benchmark):
result = benchmark(iterate_generic_uncompressed,
os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
assert result == 164
def test_iterate_parsed_compressed(benchmark):
result = benchmark(iterate_parsed_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
assert result == 164
def test_iterate_parsed_uncompressed(benchmark):
result = benchmark(iterate_parsed_uncompressed,
os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
assert result == 164
def test_iterate_file_compressed(benchmark):
result = benchmark(iterate_file_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
assert result == 164
def test_iterate_file_uncompressed(benchmark):
result = benchmark(iterate_file_uncompressed,
os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
assert result == 164
def test_read_python_large_compressed(benchmark):
result = benchmark(read_python_compressed, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
assert result == 100000
def test_read_python_large_uncompressed(benchmark):
result = benchmark(read_python_uncompressed, os.path.join(
TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
assert result == 100000
def test_fetch_plain(benchmark):
result = benchmark(fetch_plain, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
assert result == 100000
def test_fetch_parsed(benchmark):
result = benchmark(fetch_parsed, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
assert result == 100000
def test_iterate_generic_large_compressed(benchmark):
result = benchmark(iterate_generic_compressed, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
assert result == 100000
def test_iterate_generic_large_uncompressed(benchmark):
result = benchmark(iterate_generic_uncompressed, os.path.join(
TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
assert result == 100000
def test_iterate_parsed_large_compressed(benchmark):
result = benchmark(iterate_parsed_compressed, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
assert result == 100000
def test_iterate_parsed_large_uncompressed(benchmark):
result = benchmark(iterate_parsed_uncompressed, os.path.join(
TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
assert result == 100000
def test_iterate_file_large_compressed(benchmark):
result = benchmark(iterate_file_compressed, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
assert result == 100000
def test_iterate_file_large_uncompressed(benchmark):
result = benchmark(iterate_file_uncompressed, os.path.join(
TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
assert result == 100000
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